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Besides the Football War you mention, the only instance I know of that a football game influenced an actual war is case #10 listed below, the 1990 Red Star vs. Dinamo game in Zagreb. Here is a list of ten games that featured violent outcomes:
2012, Port Said-Cairo match in Egypt saw over 70 people killed accompanied by massive riots and burning down of the stadium and nearby buildings.
1985 European Cup Final, Heysel Stadium, Brussels. Liverpool and Juventus fans fought a pitched battle resulting in 39 dead and over 350 injured.
In 2012, a match between FC Olympiakos and FC Panathinaikos in Greece featured a large riot in which the fans set the stadium on fire and injured 9 police.
At the 1974 UEFA Cup Final, Tottenham Hotspur vs Feyenoord, angry English fans rioted, doing significant damage to the stadium.
In 1985, Birmingham vs. Leeds a massive riot erupted resulting in property damage.
At the Turkish League championship in Istanbul in 2012 Fenerbahce fans rioted and started setting fires in the stadium and in the vicinity. One man was seriously injured.
In 2013, the Czech Cup had to be postponed when the fans of opposing teams started a massive brawl and riot.
The 2003 WrocΕaw football riot featured an armed battle between opposing fans in which one person was killed and dozens injured.
The famous Kennilworth Road riot of 1985 occurred after a match between Millwall vs. Luton match in England. 47 people were injured.
In Zagreb in 1990 the match between Dinamo and Red Star turned into a violent brawl that ended in the stadium being torched. The event was considered a factor in the genesis of the Yugoslavian civil war that broke out the next year.